The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes

Retrotransposons comprise a large portion of mammalian genomes. They contribute to structural changes and more importantly to gene regulation. The expansion and diversification of gene families have been implicated as sources of evolutionary novelties. Given the roles retrotransposons play in genomes, their contribution to the evolution of gene families warrants further exploration. In this study, we found a significant association between two major retrotransposon classes, LINEs and LTRs, and lineage-specific gene family expansions in both the human and mouse genomes. The distribution and diversity differ between LINEs and LTRs, suggesting that each has a distinct involvement in gene family expansion. LTRs are associated with open chromatin sites surrounding the gene families, supporting their involvement in gene regulation, whereas LINEs may play a structural role promoting gene duplication. Our findings also suggest that gene family expansions, especially in the mouse genome, undergo two phases. The first phase is characterized by elevated deposition of LTRs and their utilization in reshaping gene regulatory networks. The second phase is characterized by rapid gene family expansion due to continuous accumulation of LINEs and it appears that, in some instances at least, this could become a runaway process. We provide an example in which this has happened and we present a simulation supporting the possibility of the runaway process. Altogether we provide evidence of the contribution of retrotransposons to the expansion and evolution of gene families. Our findings emphasize the putative importance of these elements in diversification and adaptation in the human and mouse lineages.

Yazar Janousek, Vaclav
Laukaitis, Christina M.
Yanchukov, Alexey
Karn, Robert C.
Yayın Türü Article
Tek Biçim Adres https://hdl.handle.net/20.500.12628/3669
Tek Biçim Adres 10.1093/gbe/evw192
Konu Başlıkları gene families
transposable elements
retrotransposons
LINE
LTR
SINE
Koleksiyonlar Araştırma Çıktıları | WoS | Scopus | TR-Dizin | PubMed | SOBİAD
PubMed İndeksli Yayınlar Koleksiyonu
WoS İndeksli Yayınlar Koleksiyonu
Dergi Adı GENOME BIOLOGY AND EVOLUTION
Dergi Cilt Bilgisi 8
Dergi Sayısı 9
Sayfalar 2632 - 2650
Yayın Yılı 2016
Eser Adı
[dc.title]
The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes
Yazar
[dc.contributor.author]
Janousek, Vaclav
Yazar
[dc.contributor.author]
Laukaitis, Christina M.
Yazar
[dc.contributor.author]
Yanchukov, Alexey
Yazar
[dc.contributor.author]
Karn, Robert C.
Yayın Yılı
[dc.date.issued]
2016
Yayıncı
[dc.publisher]
OXFORD UNIV PRESS
Yayın Türü
[dc.type]
article
Özet
[dc.description.abstract]
Retrotransposons comprise a large portion of mammalian genomes. They contribute to structural changes and more importantly to gene regulation. The expansion and diversification of gene families have been implicated as sources of evolutionary novelties. Given the roles retrotransposons play in genomes, their contribution to the evolution of gene families warrants further exploration. In this study, we found a significant association between two major retrotransposon classes, LINEs and LTRs, and lineage-specific gene family expansions in both the human and mouse genomes. The distribution and diversity differ between LINEs and LTRs, suggesting that each has a distinct involvement in gene family expansion. LTRs are associated with open chromatin sites surrounding the gene families, supporting their involvement in gene regulation, whereas LINEs may play a structural role promoting gene duplication. Our findings also suggest that gene family expansions, especially in the mouse genome, undergo two phases. The first phase is characterized by elevated deposition of LTRs and their utilization in reshaping gene regulatory networks. The second phase is characterized by rapid gene family expansion due to continuous accumulation of LINEs and it appears that, in some instances at least, this could become a runaway process. We provide an example in which this has happened and we present a simulation supporting the possibility of the runaway process. Altogether we provide evidence of the contribution of retrotransposons to the expansion and evolution of gene families. Our findings emphasize the putative importance of these elements in diversification and adaptation in the human and mouse lineages.
Açıklama
[dc.description]
WOS: 000384307900001
Açıklama
[dc.description]
PubMed: 27503295
Kayıt Giriş Tarihi
[dc.date.accessioned]
2019-12-23
Açık Erişim Tarihi
[dc.date.available]
2019-12-23
Yayın Dili
[dc.language.iso]
eng
Konu Başlıkları
[dc.subject]
gene families
Konu Başlıkları
[dc.subject]
transposable elements
Konu Başlıkları
[dc.subject]
retrotransposons
Konu Başlıkları
[dc.subject]
LINE
Konu Başlıkları
[dc.subject]
LTR
Konu Başlıkları
[dc.subject]
SINE
Haklar
[dc.rights]
info:eu-repo/semantics/openAccess
ISSN
[dc.identifier.issn]
1759-6653
İlk Sayfa Sayısı
[dc.identifier.startpage]
2632
Son Sayfa Sayısı
[dc.identifier.endpage]
2650
Dergi Adı
[dc.relation.journal]
GENOME BIOLOGY AND EVOLUTION
Dergi Sayısı
[dc.identifier.issue]
9
Dergi Cilt Bilgisi
[dc.identifier.volume]
8
Tek Biçim Adres
[dc.identifier.uri]
https://dx.doi.org/10.1093/gbe/evw192
Tek Biçim Adres
[dc.identifier.uri]
https://hdl.handle.net/20.500.12628/3669
Görüntülenme Sayısı ( Şehir )
Görüntülenme Sayısı ( Ülke )
Görüntülenme Sayısı ( Zaman Dağılımı )
Görüntülenme
4
09.12.2022 tarihinden bu yana
İndirme
1
09.12.2022 tarihinden bu yana
Son Erişim Tarihi
09 Şubat 2024 08:44
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Tıklayınız
families family expansion genomes runaway process evolution contribution findings between involvement characterized supporting expansions structural regulation diversification retrotransposons provide genome especially networks putative suggest regulatory reshaping utilization deposition undergo elevated importance second elements adaptation lineages
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